Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3); L-aminoadipate-semialdehyde dehydrogenase (EC 1.2.1.31) (characterized)
to candidate Pf1N1B4_2417 Betaine aldehyde dehydrogenase (EC 1.2.1.8)
Query= BRENDA::P49419 (539 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2417 Length = 490 Score = 218 bits (554), Expect = 5e-61 Identities = 143/458 (31%), Positives = 237/458 (51%), Gaps = 21/458 (4%) Query: 71 PANNEPIARVRQASVADYEETVKKAREAWKIWADIPAPKRGEIVRQIGDALREKIQVLGS 130 PAN E +A V++A+ D E V A + KIWA + A +R I+R+ D LRE+ L + Sbjct: 29 PANGEVLATVQRATKEDVERAVVSAEKGQKIWAAMTAMERSRILRRAVDILRERNDELAA 88 Query: 131 LVSLEMGKILVEG-VGEVQEYVDICDYAVGLSRMIGGPILPSERSGHALIEQWNPVGLVG 189 L +L+ GK E ++ D+ +Y GL I G +P + + P+G+V Sbjct: 89 LETLDTGKAYSETRYVDIVTGADVLEYYAGLVPAIEGEQIPLRTTSFVYTRR-EPLGIVA 147 Query: 190 IITAFNFPVAVYGWNNAIAMICGNVCLWKGAPTTSLISVAVTKIIAKVLEDNKLPGAICS 249 I A+N+P+ + W +A A+ GN ++K + TSL ++ +A++ + LP + + Sbjct: 148 GIGAWNYPIQIALWKSAPALAAGNAMIFKPSEVTSLTTLK----LAEIYTEAGLPAGVFN 203 Query: 250 -LTCGGADIGTAMAKDERVNLLSFTGSTQVGKQVGLMVQERFGRSL----LELGGNNAII 304 LT G ++GT + + R+ +SFTG T GK+V + G SL +ELGG + +I Sbjct: 204 VLTGSGREVGTWLTEHPRIEKISFTGGTDTGKKV---MASASGSSLKDVTMELGGKSPLI 260 Query: 305 AFEDADLSLVVPSALFAAVGTAGQRCTTARRLFIHESIHDEVVNRLKKAYAQIRVGNPWD 364 F+DADL +A+ A ++GQ CT R+F+ + ++ + A+IRVGNP D Sbjct: 261 IFDDADLDRAADTAMMANFYSSGQVCTNGTRVFVPSHLKAAFEAKIVERVARIRVGNPED 320 Query: 365 PNVLYGPLHTKQAVSMFLGAVEEAKKEGGTVVYGGKVMD----RPGNYVEPTIVTGLGHD 420 N +GPL + + LG + + K+EG ++ GG + G +V PT+ T + Sbjct: 321 ENTNFGPLVSFAHMESVLGYIAKGKEEGARLLCGGDRLTDGEFAKGAFVAPTVFTDCTDE 380 Query: 421 ASIAHTETFAPILYVFKFKNEEEVFAWNNEVKQGLSSSIFTKDLGRIFRWLGPKGSDCGI 480 +I E F P++ + ++ EEEV N+ + GL++ + TKDL R R + + GI Sbjct: 381 MTIVREEIFGPVMSILTYETEEEVIRRANDTEFGLAAGVVTKDLNRAHRVI--HQLEAGI 438 Query: 481 VNVNIPTSGAEIGGAFGGEKHTGGGRESGSDAWKQYMR 518 +N ++ GG K +G GRE+G + + R Sbjct: 439 CWIN-AWGESDAKMPVGGYKQSGVGRENGISSLNNFTR 475 Lambda K H 0.318 0.136 0.417 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 668 Number of extensions: 39 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 539 Length of database: 490 Length adjustment: 35 Effective length of query: 504 Effective length of database: 455 Effective search space: 229320 Effective search space used: 229320 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 52 (24.6 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory